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REAGENTS FOR PREPARING STRUCTURE-FREE DNA AND RNA

Award Number: R42GM074564
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 07/01/2005
PERIOD OF PERFORMANCE END DATE: 12/31/2007

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REAGENTS FOR PREPARING STRUCTURE-FREE DNA AND RNA - DESCRIPTION (provided by applicant): Secondary structure in single-stranded ONA and RNA is a significant barrier to the efficient hybridization of short oligonucleotide probes. While some probes to a given target hybridize efficiently, other probes to the same target may not hybridize at all. Use of longer probes, on the order of 60 nucleotides in length, is one way to overcome this problem. Unfortunately, such probes cannot be used to directly detect single nucieotide polymorphisms or point mutations. Use of pseudo-complementary (pc) DNA or RNA targets that lack secondary structure should facilitate the use of short probes and enable the development of generic oligonucleotide microarrays wherein every permutation of a short probe (e.g., an 8-mer) is represented on the array. Such arrays are ideally suited to the resequencing of DNA for SNP identification and to the acquisition of genetic profiles for identification purposes. We have shown that nucleoside triphosphates (NTPs) of 2-aminoadenine (nATP) and 2-thiothymine/2-thiouracii (sTTP/sUTP) can be enzymatically incorporated into DNA or RNA. These bases are pseudo-complementary since they don't interact with each other but can individually pair to the regular base complement. In this Phase I proposal we will evaluate whether dNTP analogues of dGTP and dCTP can be used together with dnATP and dsTTP in a primer extension assay to generate structure-free single-stranded DNA that can hybridize to short DNA or RNA probes with high efficiency and specificity. Existing data from ourselves and others indicate that this goal should be readily attainable and would form the basis for evaluating pseudo-complementary DNA and RNA targets for use in conjunction with short probes in a microarray format.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2007 ( Subtotal = $372,859 )
2007	2007	TRILINK BIOTECHNOLOGIES INC	9955 MESA RIM ROAD	SAN DIEGO	CA	92121	SAN DIEGO	USA	Biomedical Research and Research Training	000	3	12/14/2006	NON-COMPETING CONTINUATION	$372,859
														Subtotal = $372,859

Issue Date FY: 2006 ( Subtotal = $374,471 )
2006	2006	TRILINK BIOTECHNOLOGIES INC	9955 MESA RIM ROAD	SAN DIEGO	CA	92121	SAN DIEGO	USA	Biomedical Research and Research Training	000	2	12/23/2005	EXTENSION WITH OR WITHOUT FUNDS	$374,471
														Subtotal = $374,471

Issue Date FY: 2005 ( Subtotal = $99,871 )
2005	2005	TRILINK BIOTECHNOLOGIES INC	9955 MESA RIM ROAD	SAN DIEGO	CA	92121	SAN DIEGO	USA	Biomedical Research and Research Training	000	1	6/27/2005	NEW	$99,871
														Subtotal = $99,871

Grand Total All Awards = $847,201

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REAGENTS FOR PREPARING STRUCTURE-FREE DNA AND RNA

Award Number: R42GM074564

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 07/01/2005

PERIOD OF PERFORMANCE END DATE: 12/31/2007

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